GaiLab

2018

1. Ultrafast Hydrogen-Bonding Dynamics in Amyloid Fibrils. Pazos, I.; Ma, J.; Mukherjee, D.; Gai, F. J. Phys. Chem. B., 2018, Article ASAP. DOI:10.1021/acs.jpcb.8b04642
2. Microscopic Insight into the Protein Denaturation Action of Urea and Its Methyl Derivatives. Ding, B.; Yang, L.; Mukherjee, D.; Chen, J.; Gao, Y.; Gai, F. J. Phys. Chem Lett., 2018, 9, 11, 2933-2940. DOI:10.1021/acs.jpclett.8b00960
3. Design of a short thermally stable alpha helixembedded in a macrocycle. Wu, H.; Acharyya, A.; Wu, Y.; Liu, L.; Jo, H.; Gai, F.; DeGrado, W. F. ChemBioChem., 2018, 19, 902-906. DOI:10.1002/cbic.201800026
4. 7-Cyanoindole fluorescence as a local hydration reporter: application to probe the microheterogeneity of nine water-organic binary mixtures. Mukherjee, D.; Ortiz Rodriguez, L. I.; Hilaire, M. R.; Troxler, T.; Gai, F. Phys. Chem. Chem. Phys, 2018, Advance Article. DOI:10.1039/C7CP07160D
5. Possible Existence of α-Sheets in the Amyloid Fibrils Formed by a TTR105-115 Mutant. Hilaire, M. R.; Ding, B.; Mukherjee, D.; Chen, J.; Gai. F. J. Am. Chem. Soc., 2018, 140(2), 629-635. DOI:10.1021/jacs.7b09262

2017

1. Fermi resonance as a means to determine the hydrogen-bonding status of two infrared probes. Rodgers, J.; Abaskharon, R. M.; Ding, B.; Chen, J.; Zhang, W.; Gai, F. Phys. Chem. Chem. Phys, 2017, 19, 16144-16150. DOI:10.1039/C7CP02442H
2. Solvent Dependence of Cyanoindole Fluorescence Lifetime. Hilaire, M. R.; Mukherjee, D.; Troxler, T.; Gai, F. Chem. Phys. Lett., 2017, 685, 133-138. DOI:doi.org/10.1016/j.cplett.2017.07.038
3. Blue fluorescent amino acid for biological spectroscopy and microscopy. Hilaire, M. R.; Ahmed, I.A.; Lin, C. W.; Jo, H.; DeGrado,W. F.; Gai, F. Proc. Natl. Acad. Sci. USA, 2017, Early Edition. DOI:10.1073/pnas.1705586114
4. A 31-residue peptide induces aggregation of tau's microtubule-binding region in cells. Stöhr, J.; Wu, H.; Nick, M.; Wu, Y.; Bhate, M.; Condello,C.; Johnson, N.; Rodgers, J.; Lemmin, T.; Acharya, S.; Becker, J.; Robinson, K.; Kelly, M. J. K.; Gai, F.; Stubbs, G.; Prusiner, S. B.; DeGrado,W. F. Nature Chem., 2017 Published Online.
5. Isotope-labeled aspartate sidechain as a non-perturbing infrared probe: Application to investigate the dynamics of a carboxylate buried inside a protein. Abaskharon, R. M.; Brown, S. P.; Zhang, W.; Chen, J.; Smith, A. B.; Gai, F. Chem. Phys. Lett., 2017, In Press.DOI:https://doi.org/10.1016/j.cplett.2017.03.064
6. Activation pH and Gating Dynamics of Influenza A M2 Proton Channel Revealed by Single-Molecule Spectroscopy. Lin, C. W.; Mensa, M.; Barniol-Xicota, M.; DeGrado, W. F.; Gai, F. Angew. Chem. Int. Ed., 2017, 56, 1–6. DOI:10.1002/anie.201701874
7. Microscopic nucleation and propagation rates of an alanine-based α-helix. Lin, C. W.; Gai, F. Phys. Chem. Chem. Phys., 2017, 19, 5028-5036. DOI:10.1039/C6CP08924K
8. Do guanidinium and tetrapropylammonium ions specifically interact with aromatic amino acid side chains? Ding, B.; Mukherjee, D.; Chen, J.; Gai, F. Proc. Natl. Acad. Sci. USA, 2017, 114, 1003-1008. DOI:10.1073/pnas.1618071114
9. Simple method to introduce an ester infrared probe into proteins. Ahmed, I.A.; Gai, F. Protein Sci., 2017, 26, 375-381. DOI: 10.1002/pro.3076

2016

1. Infrared and fluorescence assessment of the hydration status of the tryptophan gate in the influenza A M2 proton channel. Markiewicz, B. N.; Lemmin, T.; Zhang, W.; Ahmed, I. A.; Jo, H.; Fiorin, G.; Troxler, T.; DeGrado, W. F.; Gai, F. Phys. Chem. Chem. Phys. 2016, 18, 28939-28950. DOI: 10.1039/C6CP03426H
2. Exciton CD Couplet Arising From Nitrile-Derivatized Aromatic Residues as a Structural Probe of Proteins. Mukherjee, D.; Gai, F. Anal. Biochem. 2016, 507, 74-78. DOI: doi:10.1016/j.ab.2016.05.017
3. Infrared and Fluorescence Assessment of Protein Dynamics: From Folding to Function. Ding, B.; Hilaire, M. R.; Gai, F. J. Phys. Chem. B 2016, 120, 5103-5113. DOI: 10.1021/acs.jpcb.6b03199
4. Meandering Down the Energy Landscape of Protein Folding: Are We There Yet? Abaskharon, R. M.; Gai, F. Biophys. J. 2016, 110, 1924-1932. DOI: doi:10.1016/j.bpj.2016.03.030
5. Kinetic Isotope Effect Provides Insight into the Vibrational Relaxation Mechanism of Aromatic Molecules: Application to Cyano-phenylalanine. Rodgers, J. M.; Zhang, W.; Bazewicz, C. G.; Chen, J.; Brewer, S. H.; Gai, F. J. Phys. Chem. Lett. 2016, 7, 1281−1287. DOI: 10.1021/acs.jpclett.6b00325
6. C≡N stretching vibration of 5-cyanotryptophan as an infrared probe of protein local environment: what determines its frequency? Zhang, W.; Markiewicz, B. N.; Doerksen, R. S.; Smith, A. B., III; Gai, F. Phys. Chem. Chem. Phys. 2016, 18, 7027-7034. DOI: 10.1039/C5CP04413H
7. Direct measurement of the tryptophan-mediated photocleavage kinetics of a protein disulfide bond. Abaskharon, R. M.; Gai, F. Phys. Chem. Chem. Phys. 2016. DOI: 10.1039/c6cp00865h
8. Utility of 5 Cyanotryptophan Fluorescence as a Sensitive Probe of Protein Hydration. Markiewicz, B. N.; Mukherjee, D.; Troxler, T.; Gai, F. J. Phys. Chem. B 2016, 120, 936−944. DOI: 10.1021/acs.jpcb.5b12233

2015

1. How Sensitive is the Amide I Vibration of the Polypeptide Backbone to Electric Fields? Oh, K-I.; Fiorin, G.; Gai, F. ChemPhysChem 2015, 16, 3595-3598. DOI: 10.1002/cphc.201500777
2. Kinetics of peptide folding in lipid membranes. Oh, K-I.; Smith-Dupont, K. B.; Markiewicz, B. N.; Gai, F. Biopolymers 2015, 104, 281-290. DOI: 10.1002/bip.22640
3. Biomolecular Crowding Arising from Small Molecules, Molecular Constraints, Surface Packing, and Nano-Confinement. Hilaire, M. R.; Abaskharon, R. M.; Gai, F. J. Phys. Chem. Lett. 2015, 6, 2546-2553. DOI: 10.1021/acs.jpclett.5b00957
4. Sensing pH via p-cyanophenylalanine fluorescence: Application to determine peptide pKa and membrane penetration kinetics. Pazos, I. M.; Ahmed, I. A.; Berríos, M. I. L..; Gai, F. Anal. Biochem. 2015, 483, 21-26. DOI: 10.1016/j.ab.2015.04.026
5. Kinetics of Exchange between Zero-, One-, and Two-Hydrogen-Bonded States of Methyl and Ethyl Acetate in Methanol. Chuntonov, L.; Pazos, I. M.; Ma, J.; Gai, F. J. Phys. Chem. B 2015, 119, 4512-4520. DOI: 10.1021/acs.jpcb.5b00745
6. p-Cyanophenylalanine and Selenomethionine Constitute a Useful Fluorophore-Quencher Pair for Short Distance Measurements: Application to Polyproline Peptides. Mintzer, M. R.; Troxler, T.; Gai, F. Phys. Chem. Chem. Phys. 2015, 17, 7881-7887. DOI: 10.1039/C5CP00050E
7. Site-Specific Infrared Probes of Proteins. Ma, J.; Pazos, I. M.; Zhang, W.; Culik, R. M.; Gai, F. Ann. Rev. Phys. Chem. 2015, 66, 357-377. DOI: 10.1146/annurev-physchem-040214-121802
8. Tuning the Attempt Frequency of Protein Folding Dynamics via Transition-State Rigidification: Application to Trp-Cage. Abaskharon, R. M.; Culik, R. M.; Woolley, G. A.; Gai, F. J. Phys. Chem. Lett. 2015, 6, 521-526. DOI: 10.1021/jz502654q

2014

1. Tightening up the Structure, Lighting up the Pathway: Application of Molecular Constraints and Light to Manipulate Protein Folding, Self-Assembly and Function. Markiewicz, B. M.; Culik, R. M.; Gai, F. Sci. China: Chem. 2014, 57, 1615-1624. DOI: 10.1007/s11426-014-5225-5
2. Experimental Validation of the Role of Trifluoroethanol as a Nano-Crowder. Culik, R. M.; Abaskharon, R. M.; Pazos, I. M.; Gai, F. J. Phys. Chem. B 2014, 118, 11455-11461. DOI:10.1021/jp508056w
3. 2D IR Spectroscopy Reveals the Role of Water in the Binding of Channel-Blocking Drugs to the Influenza M2 Channel. Ghosh, A.; Wang, J.; Moroz, Y. S.; Korendovych, I. V.; Zanni, M.; DeGrado, W. F.; Gai, F.; Hochstrasser, R. M. J. Chem. Phys. 2014, 140, 235105-235109. DOI: 10.1063/1.4881188
4. Microscopic Insights into the Protein-Stabilizing Effect of TMAO. Ma, J.; Pazos, I. M.; Gai, F. Proc. Natl. Acad. Sci. USA 2014, 111, 8476-8481. DOI: 10.1073/pnas.1403224111
5. Ester Carbonyl Vibration as a Sensitive Probe of Protein Local Electric Field. Pazos, I. M.; Ghosh, A.; Tucker, M. J.; Gai, F. Angew. Chem. Int. Ed. 2014, 53, 1-6. DOI: 10.1002/anie.201402011
6. How Quickly Can a Beta-Hairpin Fold from its Transition State? Markiewicz, B. N.; Yang, L.; Culik, R. M.; Gao, Y. Q.; Gai, F. J. Phys. Chem. B 2014 DOI: 10.1021/jp500774q
7. 2D IR Spectroscopy of Histidine: Probing Sidechain Structure and Dynamics via Backbone Amide I Vibration. Ghosh, A.; Tucker, M. J.; Gai, F. J. Phys. Chem. B 2014 DOI: 10.1021/jp411901m
8. Aggregation Gatekeeper and Controlled Assembly of Trpzip Beta-Hairpins. Markiewicz, B. N.; Oyola, R.; Du, D. G.; Gai, F. Biochemistry 2014, 53, 1146-1154. DOI: 10.1021/bi401568a
9. Slow Folding-Unfolding Kinetics of an Octameric Beta-Peptide Bundle. Montalvo, G. L.; Gai, F.; Roder, H.; DeGrado, W. F. ACS Chem. Biol. 2014, 9, 276-281. DOI: 10.1021/cb400621y

2013

1. Slow and Bimolecular Folding of a De Novo Designed Monomeric Protein DS119. Zhu, C.; Dai, Z. W.; Liang, H. H.; Zhang, T.; Gai, F.; Lai, L. H. Biophys. J. 2013, 105, 2141-2148. DOI:10.1016/j.bpj.2013.09.014
2. Using VIPT-Jump to Distinguish Between Different Folding Mechanisms: Application to BBL and a Trpzip. Lin, C. W.; Culik, R. M.; Gai, F. J. Am. Chem. Soc. 2013, 135, 7668-7673. DOI:10.1021/ja401473m
3. A Simple Method to Enhance the Photostability of the Fluorescence Reporter R6G for Prolonged Single-Molecule Studies. Guo, L.; Gai, F. J. Phys. Chem. A 2013, 117, 6164-6170. DOI:10.1021/jp4003643
4. Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-Cage. Culik, R. M.; Annavarapu, S.; Nanda, V.; Gai, F. Chem. Phys. 2013, 422, 131-134. DOI:10.1016/j.chemphys.2013.01.021
5. Quenching of p-Cyanophenylalanine Fluorescence by Various Anions. Pazos, I. M.; Roesch, R. M.; Gai, F. Chem. Phys. Lett. 2013, 563, 93-96. DOI:10.1016/j.cplett.2013.02.015
6. Amide I Band and Photoinduced Disassembly of a Peptide Hydrogel. Measey, T. J.; Markiewicz, B. N.; Gai, F. Chem. Phys. Lett. 2013, 580, 135-140. DOI:10.1016/j.cplett.2013.06.055
7. Assessment of Local Friction in Protein Folding Dynamics Using a Helix Cross-Linker. Markiewicz, B. N.; Jo, H.; Culik, R. M.; DeGrado, W. F.; Gai, F. J. Phys. Chem. B 2013, 117, 14688-14696. DOI:10.1021/jp409334h

2012

1. Light-Triggered Disassembly of Amyloid Fibrils. Measey, T. J.; Gai F. Langmuir 2012, 28, 12588-12592. DOI: 10.1021/la302626d
2. Native State Conformational Heterogeneity of HP35 Revealed by Time-Resolved FRET. Serrano, A. L.; Bilsel, O.; Gai, F. J. Phys. Chem. B 2012, 116, 10631-10638. DOI: 10.1021/jp211296e
3. Using Thioamides to Site-Specifically Interrogate the Dynamics of Hydrogen Bond Formation in Beta-Sheet Folding. Culik, R. M.; Jo, H.; DeGrado, W. F.; Gai, F. J. Am. Chem. Soc. 2012, 134, 8026-8029. DOI: 10.1021/ja301681v
4. Divalent Cation-Induced Cluster Formation by Polyphosphoinositides in Model Membranes. Wang, Y.; Collins, A.; Guo, L.; Smith-Dupont, K. B.; Gai, F.; Svitkina, T.; Janmey, P. A. J. Am. Chem. Soc. 2012, 134, 3387-3395. DOI: 10.1021/ja208640t
5. Spectroscopic Studies of Protein Folding: Linear and Nonlinear Methods. Serrano, A. L.; Waegele, M. M.; Gai, F. Protein Science 2012, 21, 157-170. DOI: 10.1002/pro.2006
6. Fluorescence Correlation Spectroscopy Measurements of the Membrane Protein TetA in Escherichia Coli Suggest Rapid Diffusion at Short Length Scales. Chow, D.; Guo, L.; Gai, F.; Goulian, M. PLoS One 2012, 7, e48600. DOI: 10.1371/journal.pone.0048600
7. Solute's Perspective on How TMAO, Urea, and GdnHCl Affect Water's Hydrogen Bonding Ability. Pazos, I. M.; Gai, F. J. Phys. Chem. B 2012, 116, 12473-12478. DOI: 10.1021/jp307414s

2011

1. Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules. Waegele, M. M.; Culik, R. M.; Gai, F. Journal of Physical Chemistry Letters 2011, 2, 2598-2609. DOI: 10.1021/jz201161b
2. Computational Design of a Beta-Peptide that Targets Transmembrane Helices. Shandler, S. J.; Korendovych, I. V.; Moore, D. T.; Smith-Dupont, K. B.; Streu, C. N.; Litvinov, R. I.; Billings, P. C.; Gai, F.; Bennett, J. S.; DeGrado, W. F. J. Am. Chem. Soc. 2011, 133, 12378-12381. DOI: 10.1021/ja204215f
3. Achieving Secondary Structural Resolution in Kinetic Measurements of Protein Folding: A Case Study of the Folding Mechanism of Trp-Cage. Culik, R. M.; Serrano, A. L.; Bunagan, M. R.; Gai, F. Angewandte Chemie-International Edition 2011, 50, 10884-10887. DOI: 10.1002/anie.201104085
4. Direct Assessment of the Alpha-Helix Nucleation Time. Serrano, A. L.; Tucker, M. J.; Gai, F. J Phys Chem B 2011, 115, 7472-7478. DOI: 10.1021/jp200628b
5. Diffusion as a Probe of Peptide-Induced Membrane Domain Formation. Guo, L.; Smith-Dupont, K. B.; Gai, F. Biochemistry 2011, 50, 2291-2297. DOI: 10.1021/bi102068j
6. Photoinduced Electron Transfer and Fluorophore Motion as a Probe of the Conformational Dynamics of Membrane Proteins: Application to the Influenza A M2 Proton Channel. Rogers, J. M. G.; Poishchuk, A. L.; Guo, L.; Wang, J.; DeGrado, W. F.; Gai, F. Langmuir 2011, 27, 3815-3821. DOI: 10.1021/la200480d
7. Transmembrane Orientation and Possible Role of the Fusogenic Peptide from Parainfluenza Virus 5 (PIV5) in Promoting Fusion. Donald, J. E.; Zhang, Y.; Fiorin, G.; Carnevale, V.; Slochower, D. R.; Gai, F.; Klein, M. L.; DeGrado, W. F. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 3958-3963. DOI: 10.1073/pnas.1019668108
8. Power-Law Dependence of the Melting Temperature of Ubiquitin on the Volume Fraction of Macromolecular Crowders. Waegele, M. M.; Gai, F. J. Chem. Phys. 2011, 134, 095104. DOI: 10.1063/1.3556671

2010

1. Infrared signature and folding dynamics of a helical b-peptide. G. Montalvo, M. M. Waegele, S. Shandler, F. Gai and W. F. DeGrado J. Am. Chem. Soc. 2010 132, 5616-5618.
2. Heterogeneous diffusion of a membrane-bound pHLIP peptide. L. Guo and F. Gai. Biophys. J. 2010 98, 2914-2922.
3. Diffusion as a probe of the heterogeneity in antimicrobial peptide-membrane interactions. K. B. Smith, L. Guo and F. Gai Biochemistry 2010 49, 4672-4678.
4. Computational modeling of the nitrile stretching vibration of 5-cyanoindole in water. M. M. Waegele and F. Gai. J. Phys. Chem. Lett. 2010 1, 781-786.
5. Nonnatural amino acid fluorophores for one- and two-step FRET applications. J. M. G. Rogers, L. G. Lippert, and F. Gai. Anal. Biochem. 2010 399, 182-189.
6. Photophysics of a fluorescent nonnatural amino acid: p-cyanophenylalanine. A. L. Serrano, T. Troxler, M. J. Tucker and F. Gai. Chem. Phys. Lett. 2010 487, 303-306.
7. Selective incorporation of nitrile-based infrared probes into proteins via cysteine alkylation. H. Jo, R. M. Culik, I. V. Korendovych, W. F. DeGrado, and F. Gai Biochemistry 2010 49, 10354-10356.
8. The two-dimensional vibrational echo of a nitrile probe of the villin HP35 protein. D. C. Urbanek, D. Y. Vorobyev, A. L. Serrano, F. Gai, and R. M. Hochstrasser J. Phys. Chem. Lett. 2010 1, 3311-3315.
9. Infrared study of the folding mechanism of a helical hairpin: Porcine PYY. M. M. Waegele and F. Gai Biochemistry 2010 49, 7659-7664.

2009

1. Probing the folding transition state of the villin headpiece subdomain via sidechain and backbone mutagenesis. M. R. Bunagan, J. M. Gao, J. W. Kelly, and F. Gai. J. Am. Chem. Soc. 2009 131, 7470-7476.
2. Effect of macromolecular crowding on protein folding at the secondary structure level. S. Mukherjee, M. Waegele, P. Chowdhury, L. Guo, and F. Gai. J. Mol. Biol. 2009 393, 227-236.
3. Using two fluorescent probes to dissect the binding, insertion, and dimerization kinetics of a model membrane peptide. J. Tang, H. Yin, J. Qiu, M. J. Tucker, W. F. DeGrado, and F. Gai. J. Am. Chem. Soc. 2009 131, 3816-3817.
4. Characterization of cofactor-induced folding mechanism of a zinc binding peptide using computationally designed mutants. J. Tang, S. G. Kang, J. G. Saven, and F. Gai. J. Mol. Biol. 2009 389, 90-102
5. Probing the role of hydration in the unfolding transitions of myoglobin and apomyoglobin. L. Guo, J. H. Park, T. Lee, P. Chowdhury, M. Lim, and F. Gai. J. Phys. Chem. B 2009 113, 6158-6163.
6. Effect of dehydration on the aggregation kinetics of two amyloid peptides. S. Mukherjee, P. Chowdhury, and F. Gai. J. Phys. Chem. B 2009 113, 531-535.
7. 5-cyano-tryptophan as an infrared probe of local hydration status. M. Waegele, M. J. Tucker, and F. Gai. Chem. Phys. Lett. 2009 478, 259-253.
8. A one-dimensional free energy surface does not account for two-probe folding kinetics of protein a3D. F. Liu, C. Dumont, Y. J. Zhu, W. F. DeGrado, F. Gai, and M. Gruebele. J. Chem. Phys. 2009 130, 061101.
9. Cholesterol-dependent phase seperation in cell-derived giant plasma membranes vesicles. I. Levental, F.J. Byfield, P. Chowdhury, F. Gai, T. Baumgart, and P. A. Janmey. Biochem. J. 2009 424, 163-167.

2008

1. Dissecting the membrane binding and insertion kinetics of a pHLIP peptide. J. Tang, and F. Gai.Biochemistry 2008 47, 8250-8252
2. Using an amino-acid FRET pair to probe protein unfolding: Application to the villin headpiece subdomain and the LysM domain. J. M. Glasscork, Y. J. Zhu, P. Chowdhury, J. Tang, and F. Gai. Biochemistry 2008 47, 11070-11076.
3. Denaturant induced expansion and compaction of a multi-domain protein: IgG. L. Guo, P. Chowdhury, J. M. Glasscork, and F. Gai. J. Mol. Biol 2008 384, 1029-1036
4. Folding kinetics of a naturally occurring helical peptide: Implication of the folding speed limit of helical proteins. S. Mukherjee, P. Chowdhury, M. R. Bunagan, and F. Gai. J. Phys. Chem. B 2008 112,9146-9150.
5. Probing the kinetic cooperativity of beta-sheet folding perpendicular to the strand direction. Y. Xu, M. R. Bunagan, J. Tang, and F. Gai Biochemistry 2008 47, 2064-2070.

2007

1. Infrared study of the effect of hydration on the amide I band and aggregation properties of helical peptides. S. Mukherjee, P. Chowdhury and F. Gai. J. Phys. Chem. B 2007 111, 4596-4602.
2. Fluorescence correlation spectroscopic study of serpin depolymerization by computationally designed peptides. P. Chowdhury, W. Wang, S. Lavender, M. R. Bunagan, J. W. Klemke, J. Tang, J. G. Saven, B. S. Cooperman, and F. Gai. J. Mol. Biol. 2007 369, 462-473.
3. Probing the Folding Intermediate of Rd-apocyt b562 by Protein Engineering and Infrared T-jump T. Wang, Z. Zhou, M. R. Bunagan, D. G. Du, Y. W. Bai, and F. Gai. Protein Sci. 2007 16, 1176-1183.
4. Site-specific hydration status of an amphipathic peptide in AOT reverse micelles. S. Mukherjee, P. Chowdhury, W. F. DeGrado, and F. Gai Langmuir 2007 23, 11174-11179.
5. The effect of charge-charge interactions on the kinetics of alpha-helix formation. D. G. Du, M. R. Bunagan, and F. Gai Biophys. J. 2007 93, 4076-4082.
6. Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers. J. Tang, R. S. Signarvic, W. F. DeGrado, and F. Gai Biochemistry 2007 46, 13856-13863.
7. Heterogeneous and anomalous diffusion inside lipid tubules. L. Guo, P. Chowdhury, J. Y. Fang, and F. Gai. J. Phys. Chem. B 2007 111, 14244-14249.

2006

1. Nanosecond folding dynamics of a three-stranded b-sheet. Y. Xu, P. Purkayastha, and F. Gai. J. Am. Chem. Soc. 2006 128, 15836-15842.
2. Understanding the mechanism of b-hairpin folding via F-value analysis. D. Du, M. J. Tucker, and F. Gai Biochemistry 2006 45, 2668-2578.
3. Ultrafast folding of a computationally designed Trp-cage mutant: Trp2-cage. M. R. Bunagan, X. Yang, J. G. Saven, and F. Gai J. Phys. Chem. B 2006 110, 3759-3763.
4. Strange temperature dependence of the folding rate of a 16- residue b-hairpin. Y. Xu, T. Wang, and F. Gai Chem. Phys. 2006 323, 21-27.
5. Infrared T-jump study of the folding dynamics of a-helices and b-hairpins. F. Gai, D. Du, and Y. Xu Methods of Molecular Biology 2006 350, 1-20 (Bai and Nussinov eds.).
6. Probing the kinetics of membrane-mediated helix folding. M. J. Tucker, J. Tang, and F. Gai J. Phys Chem. B 2006 110, 8105-8109.
7. Combining yeast surface display and computation for engineering coiled-coil protein stability. S. Park, Y. Xu, X. Stowell, F. Gai, J. G. Saven, and E. Boder Protein Eng. Des. Sel. 2006 19, 211-217.
8. Tuning the cooperativity of the helix-coil transition by aqueous reverse micelles. S. Mukherjee, P. Chowdhury and F. Gai J. Phys. Chem. B 2006 110, 11615-11619.
9. Truncation of a cross-linked GCN4-p1 coiled-coil leads to ultrafast folding. M. R. Bunagan, L. Cristian, W. F. DeGrado and F. Gai Biochemistry 2006 45, 10981 - 10986.
10. A Novel Fluorescent Probe for Protein Binding and Folding Studies: P-Cyano-Phenylalanine. M. J. Tucker, R. Oyola, and F. Gai Biopolymers 2006 83, 571-576.
11. Understanding the folding mechanism of an a-helical hairpin. D. Du and F. Gai Biochemistry 2006 45, 13131-13139.
12. A millisecond infrared stopped-flow apparatus. J. Tang and F. Gai Appl. Spectrosc. 2006 60, 1477-1481.

2005

1. a1-antitrypsin polymerization: a fluorescence correlation spectroscopic study. P. Purkayastha, J. W. Klemke, S. Lavender, R. Oyola, B. Cooperman, and F. Gai Biochemistry 2005 44, 2642-2649.
2. Conformational distribution of a 14-residue peptide in solution: a FRET study. M. J. Tucker, R. Oyola, and F. Gai J. Phys. Chem. B 2005 109, 4788-4795.
3. T-jump infrared study of the folding mechanism of coiled-coil GCN4-p1. T. Wang, W.L. Lau, W.F. DeGrado, and F. Gai Biophys. J. 2005 89, 4180-4187.

2004

1. Understanding the key factors that control the rate of b-hairpin folding. D. G. Du, Y. J. Zhu, C. Y. Huang, and F. Gai Proc. Natl. Acad. Sci. USA 2004 101, 15915-15920. DOI: 10.1073/pnas.0405904101
2. Folding of a three-helix bundle at the folding speed limit. T. Wang, Y. J. Zhu, and F. Gai J. Phys. Chem. B 2004 108, 3694-3697.
3. A new method for determining the conformation and orientation of membrane-binding peptides. M. J. Tucker, Z. Getahun, V. Nanda, W. F. DeGrado, and F. Gai J. Am. Chem. Soc. 2004 126, 5078-5079.
4. Determining b-sheet stability by FTIR difference spectra. T. Wang, Y. Xu, D. G. Du, and F. Gai Biopolymer 2004 75, 163-172.
5. Guiding the search for a protein's maximum rate of folding. Y. J. Zhu, X. R. Fu, T. Wang, A. Tamura, S. Takada, J. G. Saven, and F. Gai Chem. Phys. 2004 307, 99-109.
6. Length dependent helix-coil transition kinetics. T. Wang, Y. Zhu, Z. Getahun, D. G. Du, C. Y. Huang, W. F. DeGrado, and F. Gai J. Phys. Chem. B 2004 108, 15301-15310.
7. Tryptophan zipper folding kinetics via molecular dynamics and temperature-jump spectroscopy. C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande Proc. Natl. Acad. Sci. USA 2004 101, 4077-4082.
8. Laser-induced T-jump method, a nonconventional photo-releasing approach to study protein folding. Y. J. Zhu, T. Wang, and F. Gai. Chapter 9.1 in Goeldner, Givens (Eds.): Phototriggers, Photoswitches and Caged Compounds. Wiley-VCH, Verlag GmbH, Weinheim 2004.

2003

1. Infrared study of the stability and folding kinetics of a 15-residue b-hairpin. Y. Xu, R. Oyola, and F. Gai. J. Am. Chem. Soc. 2003 125, 15388-15394.
2. Ultrafast folding of a3D, a de novo designed three-helix bundle protein. Y. J. Zhu, D. O. V. Alonso, K. Maki, C-Y Huang, S. J. Lahr, V. Daggett, H. Roder, W. F. DeGrado, and F. Gai. Proc. Natl. Acad. Sci. USA 2003 100, 15486-15491.
3. Helix-coil kinetics of two 14-residue peptides. T. Wang, D. G. Du, and F. Gai. Chem. Phys. Lett. 2003 370, 842 - 848.
4. Temperature dependence of the CN stretching vibration of a nitrile-derivatized phenylalanine in water. C. Y. Huang, T. Wang, and F. Gai. Chem. Phys. Lett. 2003 371, 731- 738.
5. Using nitrile-derivatized amino acids as infrared probes of local environment. Z. Getahun, C-Y. Huang, T. Wang, B. D. Leon, W. F. DeGrado, and F. Gai. J. Am. Chem. Soc. 2003 125, 405-411.

2002

1. Light-induced helix formation. C-Y. Huang, S. He, W. F. DeGrado, D. G. McCafferty, and F. Gai. J. Am. Chem. Soc. 2002, 124, 12674-12675.
2. Helix formation via conformation diffusion search. C. Y. Huang, Z. Getahun, Y. J. Zhu, J. W. Klemke, W. F. DeGrado, and F. Gai. Proc. Natl. Acad. Sci. USA 2002, 99, 2788-2793.

2001

1. Time-resolved infrared study of the helix-coil transition using 13C labeled helical peptides. C. Y. Huang, Z. Getahun, T. Wang, W. F. DeGrado, and F. Gai. J. Am. Chem. Soc. 2001, 123, 12111-12112.
2. Temperature dependent helix-coil transition of an alanine based peptide. C. Y. Huang, J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai. J. Am. Chem. Soc. 2001, 123, 9235-9238.